According to the Mailardevpally police, Pentaiah (45), who works in a chemical factory, dumped the body of his daughter, who allegedly committed suicide on May 5 by hanging from a ceiling fan.
Pentaiah threw the body into a drain near his house on the outskirts of the city. The highly decomposed body parts were found floating in the drain on May 31.
The police said Pentaiah's son too had allegedly committed suicide last year.
There was an allegation that she was involved in a theft case.
"When the locals informed us about the floating skull, we started inquiries. It was revealed that Bhavani was missing for the past few days. We questioned the father who confessed to the act," Mailardevpally police-sub inspector J Nagachary told PTI.
The police registered a case and are investigating the matter.